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Yorodumi- PDB-1pvm: Crystal Structure of a Conserved CBS Domain Protein TA0289 of Unk... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pvm | ||||||
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Title | Crystal Structure of a Conserved CBS Domain Protein TA0289 of Unknown Function from Thermoplasma acidophilum | ||||||
Components | conserved hypothetical protein Ta0289 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / CBS domain / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermoplasma acidophilum DSM 1728 (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Zhang, R. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Xu, L. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain Authors: Proudfoot, M. / Sanders, S.A. / Singer, A. / Zhang, R. / Brown, G. / Binkowski, A. / Xu, L. / Lukin, J.A. / Murzin, A.G. / Joachimiak, A. / Arrowsmith, C.H. / Edwards, A.M. / Savchenko, A.V. / Yakunin, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pvm.cif.gz | 95.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pvm.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 1pvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/1pvm ftp://data.pdbj.org/pub/pdb/validation_reports/pv/1pvm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer consists of chain A (Mol.A) and chain B (Mol.B). |
-Components
#1: Protein | Mass: 20930.186 Da / Num. of mol.: 2 / Fragment: CBS DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic) Species: Thermoplasma acidophilum / Strain: DSM1728 / Gene: Ta0289 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HLD9 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.61 % / Description: Friedel pairs were used. | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 0.1M tris, 0.2M ammonium formate, 8% Glycerol, 24%PEG3350, 1.6M Mercury sulphate in protein,, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.013 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Jun 17, 2003 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.013 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 105550 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 10.5 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 44.06 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 5.04 / Num. unique all: 5748 / % possible all: 82.5 |
Reflection | *PLUS Highest resolution: 1.5 Å |
Reflection shell | *PLUS Mean I/σ(I) obs: 5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→37.46 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: friedel pairs were used.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.239 Å2 / ksol: 0.38879 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.3 Å2
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Refine analyze | Luzzati coordinate error free: 0.19 Å / Luzzati sigma a free: 0.11 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→37.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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